


Brave Like Soldiers

by ShaneVansen



Category: Stargate Atlantis
Genre: Angst, F/M, Romance, UST, h/c, post-ep
Language: English
Status: Completed
Published: 2010-02-28
Updated: 2010-02-28
Packaged: 2017-10-07 14:48:17
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 15,213
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/66184
Author URL: https://archiveofourown.org/users/ShaneVansen/pseuds/ShaneVansen
Summary: <blockquote class="userstuff">
              <p>Two weeks after the Asuran attack on Atlantis, Elizabeth is still severely injured and John, left in charge, has some difficult decisions to make.  Can he sacrifice a member of his team to save the city?  <i>First Strike</i> post-ep.</p>
            </blockquote>





	Brave Like Soldiers

**Author's Note:**

> (Notes relevant as of original posting to LJ in September 2007.)
> 
> This fic has been swirling around in my head since shortly after the first airing of First Strike, and somewhere towards the beginning of the summer I finally started writing it. Thirty-eight and a half pages later, and wow. I'm mostly just stunned I wrote something so long. It has plot!
> 
> Spoilers for S4 in that it makes use of a certain cast change and two short clips from SciFi's S4 promo from June. I am relatively unspoiled for the first two eps even though I know there are versions available online; please don't tell me what's coming. I'll wait 'til the official premiere on Friday. :)
> 
> Title taken from [Ever the Same](http://www.lyricsdomain.com/18/rob_thomas/ever_the_same.html) by Rob Thomas.
> 
> Please be aware that this is essentially unbetaed, since I sort of just finished it an hour or so ago and I really, really want to post it before S4 begins because I won't share it if I know it contradicts canon (my brain is weird like that). Ankareeda was kind enough to look over a not-quite-finished version and assure me that it makes sense and doesn't contradict canon thus far; Ro took the time out of her crazy busy schedule to do some quick betaing of a not-quite-finished version and offer suggestions and ask questions. Thanks, ladies! All errors are mine, and I reserve the right to come back and make changes once this fic is betaed. :)
> 
> And yes, that _is_ the end of the fic. No sequels planned. Deal with it.

John settled into the chair by Elizabeth's bedside, reaching for her hand even as his eyes flickered over the readouts of the equipment constantly monitoring her condition.In spite of his hopes, everything was exactly the same as it had been for the past two weeks.

"Hey, Elizabeth.It's me."He forced himself to keep his voice light."I don't know if you've heard yet, but Rodney's finally figured out why the engines failed.He thinks he can fix them in the next couple of days."He chuckled humourlessly."Of course, the ZPM is nearly drained so we won't be able to get very far.Rodney wants to start for Earth and hopes we'll intercept the Daedalus, but Zelenka doesn't think we'll make it that far and that we'll end up drifting in space without any way of letting Earth know where we are."He sighed."I don't know what to do.Guess I've got a couple of days to figure it out though, huh?"He paused, half hoping for a response, but of course none came.

John scrubbed a tired hand over his face."I can't do this, Lizabeth.My job is supposed to be keeping the city safe.I can't oversee repairs and mediate squabbling scientists and decide whether we should use the last bit of our power to search for an advanced civilization or try to reach the Daedalus – not alone.I need you to help me figure this stuff out.You have to wake up, Elizabeth."He squeezed her fingers, resting his other hand on her forearm."I need you to wake up," he repeated quietly, letting his eyes fall closed.

Still no response.John was beginning to doubt he'd ever get one.

With a deep sigh he rose to his feet, brushing a non-existent lock of hair off her face."I've got to go make sure Rodney gets some sleep before he starts making stupid mistakes – he's been awake for more than two days straight now and we ran out of coffee this morning.He's not a lot of fun to deal with, let me tell you."His mouth twisted into a small smile, as if he were sharing an inside joke with her."I'll see you a little bit later, okay?" With a final squeeze of her hand, he turned and headed for Rodney's lab on autopilot, already mulling over the pros and cons of McKay and Zelenka's options.

"Colonel Sheppard?"

Startled out of his reverie, John jerked around to see Dr. Keller hovering by his side."Doctor?" he said brusquely, hoping she'd take the hint that he wasn't in the mood to talk.

She either didn't notice or didn't care; more likely it was the latter, because he'd been avoiding this conversation for three days."Do you have a few minutes, Colonel?"

"Actually, I was just on my way to—"

"We can talk in my office," she interrupted, and John briefly wondered what had happened to the timid doctor who'd been so reluctant to take Carson Beckett's position.Trying to brace himself for what was coming – and knowing it was entirely futile – he followed her to her office.

"You've been to visit Dr. Weir today?"

He scowled at her."You know I have.Stop stalling.What do you want?"

Keller took a quick step backwards, the nervousness he remembered from weeks earlier returning in the face of his angry impatience.Then she squared her shoulders and met his eyes head on."As you know, there has been no change in Dr. Weir's condition, nor will there be.She's brain dead, Colonel, and there's nothing we can do about that.She's never going to wake up."She paused before adding, "You're listed as her power of attorney for when she's not on Earth."

John nodded automatically, his mind already jumping ahead to what she was about to say.God, he couldn't do this.He was never supposed to have to do this.He was the one who was constantly on the front line, always putting himself at risk.Elizabeth was supposed to stay safe on Atlantis.

He was never supposed to have to make this decision.

**

Thanks to his conversation with Keller, John was already in a foul mood by the time he reached McKay's lab.The argument he could hear from halfway down the hall didn't help.

McKay and Zelenka were shouting at each other, and John could barely understand either of them; Rodney was using a bunch of technical terms he couldn't follow and Radek was speaking half in Czech.Even his English was so heavily accented that most words were hardly recognizable.

"What the _hell_ is going on?" John bellowed from the doorway.Inside the lab, both scientists halted their shouting match to turn and face him.The silence lasted all of a few seconds before John was once again contending with both of them talking at once.

"This uneducated hack—"

"Uneducated?Just because you are too short-sighted to see that—"

"Short-sighted?I'm not the one who wants to waste what's left of the ZPM cruising the galaxy for a planet that _might_, despite _astronomical_ odds, have a civilization advanced enough to tell us where we are!"

"No, you just want to head for Earth and cross our fingers that we will intercept the Daedalus before we run out of power and drift aimlessly through space!"

"Enough!"John slammed his hand down on a lab bench, hard enough that it hurt.Both of the other men quieted and turned to face him.Zelenka's eyes were wide behind his glasses.

"What's with you?" Rodney demanded.

John glowered at him."What the hell are you two arguing about?"They started talking in unison again and John held up a hand to stop them before they could start arguing once more."Ah!One at a time.Rodney?"

"We were discussing the best use of the remaining ZPM energy.Have you made a decision yet?"

John sidestepped the question."Have you fixed the engines?"

Rodney turned defensive."It takes more than a few hours to fix something of this magnitude, even if half my team weren't morons.It'll be at least three days before we can move under our own power."

John scrubbed a hand over his face and then roughly through his hair."I'll have an answer for you by then."

"You know, Elizabeth would—"

"Well, Elizabeth's not here, is she?"John snapped at him, then regretted it an instant later as a hurt look flashed across his face.Before he could apologize, Rodney unexpectedly went on the offensive.

"You've been moping and stalking around here for two weeks now, and we've all had enough.I get that you're angry or upset or whatever but so are the rest of us and we're still doing our jobs—"

"Rodney—"

"—and seeing as someone thought it'd be best to put _you_ in charge if Elizabeth's ever incapacitated—"

"Rodney—"

"—maybe you could stop storming around with your head up your—"

"_McKay!_"

"You're not the only one who loves her!"

They stared at each other, and Rodney seemed shocked by his own words.Radek was looking from one man to the other, seeming ready to bolt at the slightest provocation.John's hands clenched at his sides, consumed by the bewildering but undeniable urge to punch his friend, and then relaxed."Keller says she's not going to wake up.She thinks it's time to let her go."

He turned and left.

**

From the chair behind Elizabeth's desk, John looked up at where Rodney was hovering in the doorway."Are you coming in or are you just going to block traffic all day?" he asked, turning back to the report he'd been reading.He frowned as he realized that he hadn't taken in a single word on the screen.

Rodney edged further into the room."Zelenka and I have an idea."

"About the engines," John said distractedly, scrolling back to the beginning of the report.

"No.About Elizabeth."

John jerked his head up to stare at him."What sort of idea?" he asked cautiously.As brilliant as McKay could be when it came to astrophysics, by no means did the man hold a medical degree.As much as John wanted to believe that there was something the doctors had overlooked, it didn't seem likely.

Rodney looked uncertain."You're not going to like this."

John fought to hide his annoyance."What's your idea, Rodney?"

"Do you remember when Elizabeth was infected by nanites last year?" John merely nodded; it wasn't something he was likely to ever forget."Well, nanites work on the molecular level.They can repair things that no other technology on Earth – or Atlantis, for that matter – can fix."

John stared at him in disbelief."You want to deliberately infect Elizabeth with the same nanites that nearly killed her."

Rodney nodded."I told you that you weren't going to like this."

John sat back in Elizabeth's chair."How will infecting her help cure her?She's not strong enough to fight them this time, McKay.They'll kill her."Technically, according to Keller at least, she was already dead, but he still refused to accept that.

"Hear me out."Rodney leaned forward in his seat, his hands beginning to gesture as he got into his explanation."In spite of what she went through, Elizabeth came out of that ordeal in better physical condition than before she was infected.Why?Because the nanites repaired any defects they encountered.They seem to be pre-programmed to restore biological matter to its prime condition."

"And you think that if we re-infect Elizabeth, they'll be able to fix what's wrong with her."

"It's possible."

"What's to stop them from killing her?"

"We do the same thing we did last time – draw them all to one area by planting a small amount of Wraith tissue and then hit them with an EM pulse."

"Elizabeth was actively fighting the nanites last time and they still nearly killed her.She's not strong enough to fight them.I don't even think she's aware of what's going on around her."It was the first time John had allowed the thought to surface.He wouldn't have guessed it could hurt so much.

"We'd only introduce a few of them.It will take longer, but it'll be safer."

"Aren't they self-replicating?"

"Zelenka thinks that if we periodically hit them with the EMP, we can keep the population under control."

"And we still have samples of the nanites."It was a statement, not a question; he, Elizabeth, and Carson had spent a lot of time discussing the possible benefits and dangers of keeping the nanites on Atlantis.

Rodney answered anyway."In stasis, yes."

John closed his eyes and leaned back.Rodney waited in uncharacteristic silence as he thought everything over, running through the possibilities. It should be such a simple decision – a chance at life versus letting her die – but there was so much more to it than that.This wasn't a choice to be made quickly.

He sighed, opening his eyes to look at Rodney."I'll let you know."

**

He ended up on Elizabeth's balcony.

John gripped the railing so hard that his knuckles cracked as he stared out at the stars far beyond the shield.This was Elizabeth's favourite place, her favourite time of day to relax, and it seemed fitting to him that he make the decision that would affect the rest of her life here.

If he didn't do anything, if he left her in the infirmary with machines keeping her body alive, one day months or years from now her body would simply… stop.From everything Keller had told him, nothing doctors could do with either Earth- or Atlantis-based technology could help her.

While Elizabeth had never talked in detail about the life she'd lived under the nanites' control, John was one of the few people in Atlantis who had clearance to access her mission report.After reading her account of a world where everything she'd known had been taken away and declared a figment of her imagination, he'd well understood her reluctance to sleep for several weeks after.He couldn't imagine putting her back in a similar situation.

Or he could do what Keller had suggested, and let her go.

John swore viciously, then dropped his head."Why the hell did you have to come up here?" he asked an Elizabeth who wasn't there to answer.

He didn't know what Elizabeth would want him to do.He only knew that he had to give her a chance.

His hand went to his radio."McKay, find Zelenka and meet me in Keller's office."

**

John sat back and let the scientists explain their idea to Dr. Keller, who looked more and more disturbed the longer they went on.He didn't much blame her; it was hard for him to comprehend what they were proposing and he'd been there the first time Elizabeth had been infected.Keller had only been on Atlantis for a few months and a lot of the weirdness he'd begun to accept as a part of his everyday life was still brand new to her.This would be a lot to take in.

Keller held up a hand when Rodney and Radek devolved into their own shorthand speech.John had often gotten frustrated when they did that."Let me get this straight.You want to deliberately inject Dr. Weir with a microscopic, robotic lifeform intent on killing her so they can replicate and try to take over the galaxy in their quest to eradicate the Wraith?"Keller looked like she thought they were all crazy.

Rodney frowned."That's an overly simplistic—"

"Yes," Radek interrupted.John was momentarily thrown; usually it was McKay doing the interrupting."That is, essentially, what we want to do."

"From what I understand, when Dr. Weir was infected by nanites the first time she was actively fighting them.All the scans we've run have registered zero brain activity.She wouldn't be able to resist them."

Rodney still looked put out."As I said, just before Zelenka so unceremoniously cut me off, the nanites should—"

"Should repair the damage to her brain as they're replicating.Yes, I heard you the first time.Forgive me if I have a hard time accepting that."

In spite of the seriousness of the meeting, John was tempted to smile.It was rare to find someone who could give as good as they got when it came to Rodney.

Rodney spluttered in the face of Keller's dismissal."It's a novel theory," Radek admitted, "but we believe it has a chance of success."

Keller closed her eyes and breathed in, slowly and deeply.When she opened her eyes, she was looking directly at John.

"You want to try this."It wasn't a question.

"Yes."

"Even though it will probably kill her."

He spread his hands, palm up."If we don't, she'll die anyway.Your diagnosis, remember?"

That gave her pause, but only for a moment."At least this way she'll go peacefully.With what you're proposing, there's no way to predict what she might go through."

"I know."God, did he know, probably better than anyone else; more often than not, he'd been the one keeping her company in the middle of the night when she couldn't sleep, because of either the nightmares or the fear she wouldn't wake up."But she deserves a chance.We owe her that much, at least."

The small office was quiet as the three men watched the doctor, waiting for her decision.Outside, John could hear the normal sounds of the infirmary; it seemed out of place, somehow.

Finally Keller sighed, and John knew they'd won."You're sure about this?" she asked.

He wasn't, not really.He was just out of options."I'm sure."

She folded her arms over her chest."Alright.How much time do you need to prepare?"

John could see the calculations happening in Rodney's head."Well, we need to set up a quarantine area, bring in the monitoring equipment, safely transport the nanites…." He continued to mutter to himself for a moment."I'd say one—"

"Three."

"Two hours ought to be enough time."

Keller nodded. "Okay.I'll prepare Dr. Weir."

And with that, the meeting seemed to be over.At a loss, John followed Radek and Rodney out of the infirmary."Anything I can do?" he asked as he trailed after them.

"As a matter of fact, there's a lot of heavy equipment that needs to be brought here from my lab…."

John sighed and thumbed his radio."Ronon, meet me in McKay's lab."

**

Two and a half hours later the quarantine area was crowded, holding all of John's team as well as Keller and Zelenka in addition to, of course, Elizabeth.She was already situated beneath the scanner, hooked up to the same monitoring equipment he remembered from the last time, and some other things he was pretty sure had never been in the infirmary before today.She looked so pale and thin lying there on the gurney, and John wanted to _do something_, anything, to help her.He was out of his depth here, however; killing a bunch of Asurans wouldn't help her, as much as it would make him feel better.This time, he had to sit back and let the others do their jobs.

John took a quick look around the room.Everyone else was occupied, paying him and Elizabeth no attention.

He reached out to brush her hair off her face."You can do this, Lizabeth, I know you can.Fight them. We'll all be here when you wake up."

He straightened to find Ronon watching him, but all the other man did was nod and turn back to Teyla.John couldn't find the energy to be embarrassed, so he just moved to join the people in charge of this experiment.

Rodney and Radek were explaining to Keller exactly what to do over the next hours.John only half-listened, partly because there was nothing he could do and partly because he'd been here the first time and he hadn't understood it then, either.

"Are we ready?" he asked when the two scientists finally stopped talking.Rodney gave him a dark look but Radek cut him off before he could respond with some snarky remark.

"I believe we are, unless you have any questions, Doctor?"He directed the last to Keller, who shook her head.

"I'm as ready as I'll ever be."John watched her pull on a pair of HazMat gloves, and caught the slightest hesitation before she reached to deactivate the stasis chamber.From inside she withdrew a vial that, John knew, contained a sample of the nanites.

He stepped up to the very edge of the quarantine tent as Keller entered, using a needle to place the nanites in one of the many tubes keeping Elizabeth alive.His eyes moved to the screens monitoring her vital signs; though he knew that, logically, there would be no instantaneous reaction, John couldn't seem to stop himself from searching for a change, any change.But there was nothing.

At his shoulder, Rodney was surprisingly gentle as he reminded John, "It'll be several hours at least before we see anything, if we do at all."

John nodded shortly."I know."

"You don't need to be here for-"

"Yes. I do."There was no room for argument in John's voice, and Rodney let it drop.

John snagged a chair from the outskirts of the room and dragged it next to the quarantine tent, positioning himself so he could keep an eye on Elizabeth and the monitors.Then he settled in to wait.

**

A sudden beeping jerked John out of a light doze and he snapped upright, his eyes darting from Elizabeth to the readouts on the screens.She was as still as ever, not appearing to have moved at all, but one of the screens was flashing something he couldn't make out."What's going on?" he demanded as he rose to his feet.To his right, Keller pulled on the HazMat gloves before rushing into the room.

Rodney checked his own equipment."The nanites have multiplied beyond what we set as the safe limit.We need to draw them all to one area and use the EMP to lower their numbers."

John stood back and let the doctor and scientists do whatever they needed to do.Before they had finished he turned and left the infirmary with the need to work off a sudden and vicious restlessness.

He went to the control room first; though he would have been paged if they'd needed him, he _was_ in charge and it'd been close to a day since he'd last set foot there.After ascertaining that everything was running smoothly – as much as could be expected, given the circumstances – he paged Teyla and asked her to meet him in the gym.

**

"You are certain you feel up to this?"

John swung his stave in a tight circle."I'm sure."

Teyla didn't look altogether convinced but she nodded anyway."Very well."She rose slightly on the balls of her feet and that was the only warning he got before she attacked.

He just barely got his sticks up in time to deflect the blow, but she had him retreating from the first strike and he never managed to regain his footing.In less than a minute he was flat on his back, gasping for breath.

Teyla stood quietly off to the side, watching."Again?" she asked when he sat up, and John nodded as he climbed to his feet.

They sparred for over an hour, John ending up on his back more often than not.By the time he was too exhausted to continue, he felt better.

"Do you wish to talk now?"

John took a quick step backwards, lowering the towel he'd been using to mop his face."What?"

Teyla regarded him from halfway across the gym."You've had a difficult few weeks, more so than usual.Have you been sleeping?"

"Not much," he admitted, then narrowed his eyes at her."I'm not going to meditate," he warned her, only half joking.

She smiled."I know better than to suggest meditation to you," she assured him before she turned serious once more."But if you ever wish to talk—"

"Thanks," he interrupted.He gathered up his belongings and headed for the exit, pausing as he passed Teyla."I do appreciate it," he said quietly, and accepted the gentle hug she gave him."I'll see you later," he told her, filling the awkward silence, and bolted for the door.

Back in his own room, he ran the shower as hot as he could stand it and learned forward, bracing his hands against the wall and letting the water pour over him without moving.He didn't know how long he stood there, or how much longer he would have stayed, if not for the sound of his name over the P.A. paging him to the infirmary.

**

Rodney frowned at him as he entered the room."What were you doing?" he asked, his eyes on John's wet hair, then shook his head."Never mind.We've got something."

"What?" John demanded, straining to take in the various readouts.

It was Keller who answered."There's brain activity."She held up a hand as if to forestall comments."It's not a lot.There's weak activity in the brain stem, which regulates autonomic functions such as heartbeat and breathing, but it's not enough to sustain her body on its own.There is no indication of activity in regions used for higher-order thinking."Her voice softened."That being said, regaining activity in the brain stem is unheard of.Whatever these nanites are doing, they might actually be repairing the damage her brain suffered."

That was a lot for John to process so he boiled it down to what he needed to know."This is good, right?"

For the first time that John could remember, Keller smiled."I think it is, Colonel."

And for the first time in more than two weeks, John smiled too.

**

It took nearly three more days before Keller announced that Elizabeth's brainwaves had returned almost to normal.Over the course of those days, John had split his time between the control room, the labs, and the infirmary, catching a few hours of sleep when he could.He was busy supervising everything but he felt useless nonetheless because he wasn't directly responsible for any of it; he just got the reports.John never thought he'd be jealous of scientists.

On that third day, John was present when Keller summoned Rodney and Radek to the isolation room to remove all of the nanites from Elizabeth's system. It took repeated pulses from the machine, enough that the scientists seemed worried that they'd never get them all, but eventually the two declared the procedure successful.

The doctor ran a ton of tests while John waited impatiently.After several long hours, Keller sat him down to walk him through the results.

"This," she began, drawing his attention to the computer screen, "is a scan of Dr. Weir's brain activity from last year.Dr. Beckett used it to confirm that Phoebus' imprint had faded completely."

"This scan," she continued, bringing up a second image alongside the first, "is from last week.There is no noticeable activity."

"And this one-" a third image appeared beside the other two, "-is from a few hours ago."

John sat back in the chair, studying the monitor.The most recent scan, while not exactly the same, closely resembled the one from a year ago."So, she's better?"

Keller hesitated before answering and John felt his cautious hope sinking."'Better' is a relative term, Colonel.Certainly there is improvement from just a few days ago and I would have thought this sort of recovery impossible if I hadn't witnessed it for myself.That being said, however," she added, and John braced himself for what was coming next, "we really understand very little about how the human brain works, and even less about the effects the nanites may have had."

"Just tell me where we stand," John ordered tiredly.He probably wouldn't understand half of this on a good day, and with as little sleep he'd had lately he didn't even have the energy to try.

Keller nodded, looking sympathetic."If she wakes up, it looks like she should make a full recovery, or close to it.There's still a chance of brain damage, or other changes that wouldn't necessarily show up in a scan, such as a personality disorder.There's no way to know for sure until she's awake."

"And when will that be?"

The doctor shrugged."Physically, I can see no reason for her to still be comatose.She'll wake up when she's ready."

John was growing sick and tired of all the uncertainty.Rodney's opinion of the medical profession was suddenly making a lot of sense."Can I sit with her?" he asked, hearing the edge in his voice.

Keller nodded."Dr. McKay checked for nanites less than an hour ago and found none.She should be out of the iso room by now."

**

John eased into the infirmary chair and wrapped his fingers around Elizabeth's, unexpectedly comforted by the return of a ritual interrupted by her stay in isolation."Hi, Elizabeth.Sorry I haven't been around the last few days, but you were kind of infected by nanites and they wouldn't let me in to see you.Imagine that, huh?"The corners of his mouth turned up in the faint hint of a smile.

"So," he continued, carrying on with his one-sided conversation."Dr. Keller says there's no reason why you can't wake up.Now, I'm not really convinced she knows what she's talking about most of the time, but I happen to agree with her about this.You'll wake up when you're ready; you just have to decide it's what you want.We all know how stubborn you can be when you don't want to do something, but you always take other people's opinions into account before making a final decision, and I gotta say, Lizabeth, in my professional opinion, you really should wake up soon.Right now, even, but I can understand if you want to take a few minutes."John squeezed her hand, carefully studying her face for any sort of reaction.He was disappointed but not especially surprised when there was no change.

He sighed."Alright, we'll do it your way.But I can only stay for a little while; this city doesn't run itself, you know, and seeing as you've spent the last three weeks lying around in bed, I get stuck with the job."John made himself more comfortable, suddenly aware of how much he was rambling to an unconscious woman.He blamed three weeks of stress and sleeplessness and the sudden gratification of knowing that Elizabeth had a fighting chance.Whatever the reason, he'd never hear the end of it if Ronon or Rodney overheard him.

Still holding her hand, John waited.

**

"Sheppard?"

John jerked upright, apparently having dozed off."What?" he grunted, scrubbing a hand over his face.His eyes instinctively drifted over Elizabeth's face and the monitors keeping track of her condition.

Ronon loomed over the end of the hospital bed."McKay sent me to find you when you didn't answer the radio."

John's hand went automatically to his ear.Not finding his headset he scanned the floor, catching sight of it by the chair."Must've fallen out," he said, retrieving it."What does Rodney want?"

Ronon moved to the far side of the gurney, facing John over Elizabeth's prone form."How is she?" he asked, touching her forearm with a gentleness that seemed incongruous with the large man.

"The same," John responded, stretching muscles that ached from being in the same position for too long."Keller seems to think she could wake up any minute, or she could never wake up at all.There's no way to know."Ronon nodded, still stroking Elizabeth's arm.John blinked."What'd McKay want?" he asked.

"Said the engines are fixed and it's time for you to make a decision.I assume you know what he means."

"Yeah," John muttered.He'd nearly forgotten about that."I guess I better head down there before he and Zelenka start arguing again."Straightening his sleep-rumpled clothes, John headed for the exit.

"What's that mean?"

"What's what mean?"

"The change in the beeping."

John spun back around, eyes zeroing in on the monitors; he hadn't caught any difference in the sounds of the equipment, but Ronon hadn't evaded the Wraith for seven years by missing the small details."Which one?" he demanded.Ronon gestured at one of the screens.John studied the readings, wondering if he was imagining the changes he thought he saw.

He strode up to the gurney, sliding his hand into Elizabeth's."Elizabeth?" he prompted, his other hand coming to rest on her forearm."Can you hear me?Squeeze my hand."No reaction."C'mon, Lizabeth.Ronon and I are right here, and you've got an entire city waiting for you to wake up.All you have to do is squeeze my hand."John held his breath, silently willing her to wake up, but there was nothing.

Disappointed, he was about to pull away when he thought he felt the flutter of her fingers against his.Not entirely certain it wasn't just wishful thinking, he coaxed, "Once more, Elizabeth.I need you to do that just one more time."It took a few seconds but then her fingers unmistakably pressed against his.

"I felt it too."

John looked across the bed to see that Ronon had taken Elizabeth's other hand."Good enough for me," he said, then hollered, "Doc!" over his shoulder.

A nurse stuck his head past the curtain."Is there something wrong, Colonel?" he asked.

"She's waking up.Get Keller in here."He leaned over her, his hand still in hers."Time to open those eyes, Elizabeth.Just for a second.I know you can do it."Her eyes moved back and forth beneath her lids, eyebrows drawing together in a frown.She cracked them open the tiniest bit but immediately closed them again with a small sound that John took as discomfort."I know that's got to be bright.We'll get someone to turn down the lights, okay?"She didn't respond but the frown faded from her face.

John glanced at Ronon as Keller entered and moved straight to the monitors, taking them in with one look before shifting attention to Elizabeth."Can you let Rodney know she's awake?" John quietly asked his teammate as he watched the doctor.Ronon nodded and left the room.

John tried to stay out of Keller's way as she did some sort of assessment on Elizabeth, asking her to squeeze her hand and using a penlight to check her pupils.Keller then turned her attention back to the monitors for a moment.His eyes never left Elizabeth's face for more than a few seconds.

"Dr. Weir, can you open your eyes?"There was no response and John watched as the doctor frowned and checked the monitors yet again.Then she took her penlight and shone it in each of Elizabeth's eyes once more.

"What's wrong?" John asked sharply, moving closer and sliding his hand into Elizabeth's.He called her name but got no response.

"She's asleep," Keller reassured him."It's just a normal, healing sleep.She'll wake up on her own in a few hours or so."

John relaxed, stroking his thumb over her knuckles."It's good that she woke up, right?She's going to be okay?"

There was a moment of silence before she sighed."That she woke up at all, that she responded to you... I don't know if you understand how incredible this is.By all rights, Dr. Weir was brain dead.This shouldn't be possible.If she comes through this with no physical or mental impairment it'd be, well, a miracle."

"But the nanites—"

"The nanites," Keller repeated, for all the world sounding as if she were agreeing with him.She held out her hands, palm up."I don't know what to tell you, Colonel.There's no precedent for any of this.I have no idea what will happen."

Rodney was right, John decided.Doctors were useless.

"Elizabeth's awake?"

_Speak of the devil._McKay appeared, Ronon close behind and pushing the scientist further into the room.Rodney scowled at him as he stepped to the end of the Elizabeth's bed."I thought you said she was awake," he accused Ronon once he saw she was unconscious.

"She was.She fell asleep a couple of minutes ago."John filled him in.

Rodney looked disappointed."Oh.How long until she wakes up again?"

"It'll be a few hours.Though if you keep talking that loud I don't see how she could sleep through it."

"Oh, ha ha."

"If you two don't mind, my patient is trying to sleep.Either keep it down or get out."Keller fixed each of the men with a steely look.

John motioned toward the door."Let's go talk in Elizabeth's office.You coming?" he asked Ronon, who shook his head.

"I'll stay here," he said, and John felt better knowing someone would be staying with her.

"Call me if she wakes up," he said, watching Rodney pat Elizabeth's leg before moving toward the door.Ronon just grunted in response, taking over John's spot at her side.

**

John dropped into Elizabeth's chair, Rodney settling more slowly into one of the chairs on the other side of the desk."So?"

Rodney frowned at him."So, what?"

"You were looking for me earlier?"

McKay perked up."Right! I got the engines working.They're not one hundred percent because we don't have the resources on Atlantis to bring them up to full power, but we'll be able to enter hyperspace."

"For how long?"

Rodney lost some of his excitement."There's no way of knowing for sure.A couple of hours at least, maybe as long as a full day."

"How long would it take to intercept the Daedalus?"Rodney squirmed in his seat and John became suspicious."McKay?How long?"

"I... don't know."

John blinked at the unexpected response."Best guess?"

"Don't have one."

John was confused, not to mention apprehensive."What aren't you telling me, McKay?"

Rodney spluttered for a moment and then suddenly sagged.For the first time in quite a while John noticed how tired his friend looked."We still don't know where we are.Without that information there's no way for us to know what direction to go and we can't exactly just pick a random direction and start flying."

John dropped his head into his hands for a moment."Three weeks.We've been drifting through space for _three weeks_.How do we not know where we are?"

Rodney looked annoyed."The universe is a pretty big place, Colonel.Not even the Ancients mapped it all.Add to that the fact that the computers still aren't working properly and I've had most of my team working on keeping the shields and life support stable in addition to fixing the engines, and excuse me if we've had to put figuring out our location on the back burner!"

_What good do the engines do us if we don't know where to go?_John barely refrained from snapping at Rodney, reminding himself that they were all tired and on edge."So your idea of intercepting the Daedalus isn't even an option at this point."

Rodney looked as if he wished he could argue the point."Not until we know our relative position in the universe, no.Which," he added, "we'll be able to focus on now that the engines are working."

John sighed."I gotta say, Rodney, Zelenka's option is looking more likely."He held up a hand to forestall his protests."Let's give it a few more days.No one knows we're here, including the Asurans, and we have working engines and shields.We're safe enough for the moment.A couple of days gives your team a chance to figure out where we are, and maybe by then Elizabeth will want to give her opinion."

Rodney seemed surprised."She just woke up from three weeks of being brain dead, and she'll be back to work in a few days?"

"That's not exactly what I meant.She might be more alert by then and you know Elizabeth – she'll be wanting right back in the thick of things."He couldn't help the fond smile, which Rodney shared.

The smile didn't last long, though."How's she doing?" Rodney asked soberly.

John stood, prowling around the office."I don't know.She woke up and squeezed our hands when we asked her to, and tried to open her eyes.But she didn't move otherwise and didn't say anything."He put down one of the Elizabeth's trinkets."Keller says her vital signs are good but beyond that, she can't say what Elizabeth will... be like, once she fully wakes up."He stared out the window at the people working in the control room.

"Elizabeth's strong," Rodney said eventually."I mean, she never should have made even this much improvement.If anyone can get through this, it's her."

"Yeah," John agreed softly, still watching the others in the next room.Pulling himself back, he cleared his throat and turned to face Rodney."I want the people on your team who have had the most sleep to stay in the labs; everyone else is to get something to eat and then sleep.Eight hours at least.That includes you."

"But—"

"We're not going to get anything done if everyone's starving and exhausted.We should be safe for eight more hours."

"Are you taking a break too?"

John thought of all he still needed to do, and of the woman who would be waking in a matter of hours.He rubbed a tired hand over his face."At some point.Sure."

"Go grab a few hours now," Rodney urged, unexpectedly sympathetic."You won't do her any good if you're exhausted when she wakes up.She's going to need you."John narrowed his eyes at him but Rodney only waved a hand."Oh, please.As much as she's relied on you the past few years and how much time you've spent in the infirmary the past three weeks?Like anyone doubts who's going to be by her side while she recovers."

If he weren't so tired, John thought his embarrassment might have morphed into mortification.As it was, he ignored the heat in his cheeks and glared halfheartedly at Rodney."Shut up and get some sleep, McKay.You're rambling."

Rodney clapped him awkwardly on the shoulder as he left.John surveyed the office and the control room.Deciding to follow his own advice, he headed to his room to catch a few hours of sleep.

**

When John woke, he was surprised to learn that he'd slept a solid six hours; he hadn't had that much uninterrupted sleep since before Colonel Ellis had arrived on Atlantis with plans for a pre-emptive strike against the Asurans.

He indulged in a ten-minute shower, half that time spent just standing and letting the nearly scalding water pour over him.After, a quick detour to the mess hall provided him with coffee and a bagel before he checked in with the control room.Assured that nothing had gone critical overnight and that nothing required his immediate attention, John headed where he most wanted to be.

The infirmary was mostly quiet when he entered, with a few nurses working and no sign of Keller; John wondered if she'd finally gone to get some rest as well.He made his way across the room with as little noise as possible, trying not to disturb the two patients who were still asleep.

The first thing John noticed as he slipped into Elizabeth's room was Rodney.He sat in the chair by her bed, head tilted back and mouth gaping as he snored quietly.John smiled fondly, wondering how long his friend had been there.

The second thing he noticed was a pair of familiar green eyes.

John faltered for a second, the force of seeing her awake and watching him unexpectedly fierce."Elizabeth," he all but whispered, and why the hell was he so nervous?He almost couldn't breathe.

"John."Her voice was raspy from weeks of disuse but her smile was bright and _she recognized him_.He had no idea until that moment how terrified he'd been that she wouldn't know him.

He skirted Rodney to stand beside the bed, taking her hand out of habit.She squeezed back."How are you feeling?" he asked quietly, out of deference to the sleeping man.Besides letting Rodney get some much-need rest, John selfishly wanted a few minutes alone with Elizabeth.

"I feel fine."He raised an eyebrow in disbelief."Really, I do.What happened?"

God, where to start?"What's the last thing you remember?"

Her eyes lost their focus and her forehead scrunched a little."We were launching," she said eventually."We pushed an asteroid in front of the Asurans' beam and were rising out of the atmosphere so we could take Atlantis somewhere safe."She left off there but still seemed caught up in her memories, so John stayed quiet until she shook herself and looked up at him."I take it we didn't blow up."

"We didn't.You kind of did."John pushed away the automatic guilt at not getting the city into space fast enough.

She frowned."I what?"

He eased a hip onto the gurney, their hands still entwined."We didn't get the shields up in time and the Asuran beam hit the central tower.You were—"His voice cracked.He cleared his throat before continuing."You were thrown down the stairs by the force of the blast.That was three weeks ago."

Elizabeth was pale."Three weeks," she repeated faintly.

John studied her hand in his, unable to meet her eyes."You were in a coma until last night."There was so much more that she needed to know but he needed a minute to work out how to tell her what they'd done, what Rodney had suggested and what John had allowed them to do to her.Risking a glance at her face and taking note of her pallor, he decided that maybe giving Elizabeth a few minutes would be a good idea.

They sat in silence.In the chair, Rodney snorted and shifted position but didn't wake."I should feel worse," she said suddenly, startling him."If I was blown down a flight of stairs and spent three weeks in a coma, I should feel a lot worse than I do."She was looking directly at him now.

John flipped her hand over, tracing his thumb over her palm and wondering which crease was her lifeline.Then he looked up and met her gaze."It was bad, Elizabeth.You were brain dead.Keller said there was nothing...."His voice failed him and he closed his eyes for a moment.

"Tell me."He looked at her."Tell me, John."

Sucking in a deep breath, he told her everything.

Halfway through his narrative he caught sight of Rodney waking, but he didn't interrupt as John finished the story.After, the two men sat silently and watched Elizabeth.

Her eyes were closed, her breathing a little shallower than usual and her free hand, the one not still John's, clutched the sheets tightly.

When she still hadn't spoken after a few minutes, John became concerned."Are you okay?"He ran his thumb over her palm again.

She let out a shaky breath."Yeah.I just....It's a lot to take in."

He could understand that; hell, he was still trying to understand most of it and he'd had much longer to process it all."Can I ask you something?"She lifted an eyebrow at him and John tried to phrase the question in his head before asking it aloud."The last time you were infected by these things, they tried to convince you that Atlantis never existed.Did they do anything like that this time?"His biggest fear about letting the nanites infect her again hadn't been that the procedure wouldn't work, but that she'd be trapped in a hell of their making.If the five hours she'd been pulled under the last time had seemed like months to her, then two days would have felt like years.If he'd been responsible for putting her through that—

Elizabeth shook her head slowly."I don't think so.I don't remember anything like that, although I think I remember dreaming.It's just vague images, though."

"They may come back to you, but it's more likely that even that will fade in a day or two."All three of them looked up as Keller entered the room."Though from what I understand it may be better if you don't remember.How are you feeling, Dr. Weir?"

John and Rodney ducked out as Keller started examining Elizabeth, knowing that the doctor would be running dozens of tests and it would be hours before she was through.

"You checked in with your team recently?" he asked Rodney as they headed for the control room; John had a couple of meetings in an hour and a whole pile of reports he wanted to get through before Elizabeth was freed of Keller's tests.He knew her well: she'd want to know every last detail of how her city was doing and he planned to tell her.

"Most of them were still sleeping but the team working the overnight shift continued working on figuring out where we are.We still don't know, by the way."

"Any idea when we _will_ know?"He didn't like the idea of drifting through space with no idea of where they were or how to get home.

"There's no way to tell.We could go for weeks or months without knowing, or we could find it in the database later today if we happened to gain access to the right part of the computer mainframe."Rodney shrugged, looking frustrated."The Asurans did a number on our computer – a lot of things are still scrambled and will be for some time.There's information we may never recover."

John sighed."Alright.Just... let me know when you find something."Rodney made a sound – John wasn't sure if it was a snort or a laugh – before veering off in the direction of the labs.John contemplated the size of the pile of paperwork waiting for him and decided that another cup of coffee was in order before tackling it.

**

By the time John got through the latest batch of reports and firearms practice it was nearly dinner, so he stopped by the infirmary.

Elizabeth was looking much better than she had that morning.She was sitting up, a book open in her lap, and she was much less pale than she had been just hours ago.Someone had brought her a change of clothes – not her uniform, but something more casual and definitely an improvement over the scrubs he'd gotten used to seeing her in the past three weeks.

"You're looking better," he remarked, stopping a few paces from the side of her bed.He fought the urge to be closer, to take her hand and feel the warmth of her skin, but she was awake and aware and looking so much like _herself_ that he automatically reverted to the carefully maintained distance he'd always tried so hard to keep around her.

She smiled at him, rolling her eyes a little."I wish Dr. Keller agreed.The tests all came back clear but she's insisting that I spend the night for 'observation'."He could practically hear the quotation marks around the last word.

"You hungry?"He took an unconscious step closer.

"Starving.What did you have in mind?"

"Why don't we see if Keller will spring you long enough for supper in the mess hall?"

She looked almost as thankful as she did when he'd returned safe and sound from saving Atlantis from one enemy or another.Barely a day of being conscious and she was already sick of the infirmary.He marvelled at how healed, how _whole_ she was.John never thought he'd be so grateful to nanites."Sounds good."

Surprisingly, Keller agreed to let Elizabeth leave the infirmary as long as John promised he wouldn't let her out of his sight for a second – like that was a possibility anyway – and that he'd have her back within an hour.

In the end, they took their meals to her office to eat because what seemed like the entire population of Atlantis kept stopping by their table to speak to Elizabeth.She kept up a good front and took time to talk to each person, but John saw how quickly she was tiring and got her out of there with a few well-placed warning glares.

He brought her up to date on the main points while she ate, figuring the details could wait until the next day.She took in most of it silently.

"Does Rodney have any idea how long it will take to fix the computer?" she asked when he'd finished, taking a sip of water.

"No idea.Apparently they could stumble on the solution tomorrow or it might never be repaired."

She raised an eyebrow."Let's hope it's closer to the former."

Glancing at his watch, John reluctantly stood."It's been almost an hour.We'd better get you back."

She made a face but rose, only to sway unsteadily.John was quick to support her with a hand on her hip and shoulder.

"You okay?" he asked worriedly, wondering if he should page the infirmary.

"Yeah.I guess after three weeks in bed I should expect a few side effects, hmm?"

After three weeks of being brain dead, he thought, she shouldn't even be here at all.If the worst she suffered was a head rush from standing too quickly, she was quite possibly the luckiest person in the universe.

To his surprise, she slipped her arm around his waist as they moved past the control room into the deserted corridor beyond.Tentatively he wrapped an arm around her shoulders, holding back a sigh when she leaned into him.It was just because she was tired, he knew, but he still revelled in the feeling of her so close.

He slowed as they approached the infirmary, part of him unwilling to enter the bright and busy facility; he wished he could spend just a few more minutes alone with Elizabeth to reassure himself that this was real and not just a hallucination brought on by stress and lack of sleep.

Elizabeth twisted to face him and John regretfully let his arm fall from her shoulders.She left her hand on his waist."What is it?" she asked quietly.

He wouldn't meet her gaze."Nothing."

"John?"

_Dammit_."It's just…."He shrugged as though it were nothing important."I'm glad you're okay."

Her expression softened and she moved as if to touch him, pulling back at the last moment."I wouldn't be if it weren't for you."

John couldn't say if she reached for him or he for her; all he knew was they were hugging each other in the middle of the hallway, just beyond the light spilling from the infirmary doors.Her breath was hot against his neck and he buried his face in her hair, breathing in her scent.

Elizabeth pulled away first and he let her, stepping back and clearing his throat."Breakfast at 0800?"It was something of a tradition of theirs to do their first briefing of the day over coffee and food.

She smiled."Sounds good."She leaned up then, catching him off-guard and pressing a light kiss to his cheek."Good night, John."She was gone before he could answer.

Grinning stupidly, John headed for his quarters.

**

Elizabeth ended up being discharged in time for breakfast amid Keller's disbelief that she had healed so quickly and thoroughly, but she refused to sign Elizabeth off as fit for duty.At the very least, she maintained, she would have to talk to Dr. Heightmeyer first.

Their meal was once again interrupted by a steady stream of well wishers, but Elizabeth refused to leave.John understood; they hadn't had an easy month and seeing their leader alive and well was a symbol of hope that they just might get through this.

She spent most of the day with him as he dealt with the minutiae that came with running a flying city that was lost somewhere in the universe, using the opportunity to get caught up on Atlantis' situation.He left her on the couch reading through reports when he went to meet Ronon for a sparring session, and returned two and a half hours later to find her sound asleep in much the same position.

Moving the laptop to a safer place, he dug out the blanket she kept in her office and covered with it before turning down the lights and ensuring the rest of the city knew the room was off limits.

**

Sometimes John wondered why he bothered getting the details from any of the scientists.He didn't understand most of what they told him and when he did get it, it usually seemed to be bad news.At the moment, they were telling him that Atlantis ran the risk of draining its remaining ZPM.

He glanced at Elizabeth, who was halfway across the lab frowning at a computer screen, then turned his attention back to McKay and Zelenka."What if we landed on an uninhabited planet for a while, until you guys figure out where we are and how to get home?Then we could turn off the shields and the life support."

The two scientists did that silent talking thing that John didn't usually get, but he caught the undertones even before Zelenka started speaking."It's hard to say.We would save energy by landing, yes, but the amount of power needed to lift off... it is immense.It could very well deplete our remaining power."

"How long 'til drifting through space does the same thing?"

The other two men exchanged glances again."I'd say three—"

"Five."

"—maybe four months?There are too many variables to say with any certainty."

_Four months?_John knew that the computer geeks were having trouble but he'd still figured it'd take them a few more weeks at most.Four or five months was almost inconceivable.

Thankfully, the decision no longer rested on his shoulders alone; though she hadn't officially been cleared for duty, Elizabeth would definitely want a say.

He turned to see her typing rapidly at one of the laptops scattered around the room.Her brow was creased in concentration and she was barely even blinking."Elizabeth?"She didn't respond and he called her name again, a little louder.This time she started, looking over at him and blinking rapidly as if trying to focus her gaze."What're you doing?" he asked, curious what had held her so rapt.

Elizabeth looked almost confused."I don't know."The laptop beeped suddenly and then Rodney was rushing over to stand next to her, muttering under his breath about amateurs playing with lab equipment.He tapped a few keys and then abruptly froze, jaw dropping as he stared at something on the monitor.Then he spun towards Elizabeth.

"Did you do this?"

Elizabeth shrank back in the face of Rodney's forcefulness and John took an instinctive step forward."I think so."

Rodney continued to gape at her."Do you have any idea what you've _done_?"

Now John decided to intervene."Look, McKay, I'm sure that you can fix whatever Elizabeth might have—"

"Nonononono.You don't understand.Look at this!"He spun the laptop around to face him.John squinted, halfway hoping the technical jargon would resolve itself into something recognizable.Beside him, Zelenka whispered something in Czech.He sounded awed.

He looked at the other three."Someone want to clue me in here?"

Zelenka still sounded almost reverent."She found it."

John raised an eyebrow."Found what?"He was asking the room at large but he was looking at Elizabeth.She merely stared back.

"Our position."McKay seemed stunned."She found our position in the universe relative to Pegasus and the Milky Way."

_Holy shit_.Even John understood the significance of that."How'd you do that?" he asked Elizabeth, who was starting to look a bit freaked out.

"I don't know.I saw the program running and I just sort of... knew where to look for the information.It was right where I knew it would be."

His hope they'd soon be able to head for Earth was quickly waning in the face of the implications this held for Elizabeth.A quick look at the other two men told him they were realizing the same thing: Elizabeth had just figured out in a matter of minutes what two dozen computer experts couldn't find after three weeks of exhaustive searching.While she was admittedly better with computers than he was, she still had the tech guys looking at her laptop once or twice a month.She shouldn't have been able to do what she'd done.

Elizabeth herself realized what all this might mean, because she smiled weakly at him and asked rhetorically, "I'm going to have to undergo more tests, aren't I?"

**

John woke with a start, eyes darting around the dark room as he fought to even out his breathing.Gripped by a sudden and unshakeable urge, he swung his legs over the side of his bed and headed for the door.

He hesitated outside Elizabeth's room, feeling foolish that a dream had driven him to seek her out well past midnight. Even though Keller hadn't been able to find any reason why she'd suddenly become a computer savant and didn't think there was anything to worry about, he just couldn't shake the feeling that something was wrong.Going with his gut, he knocked.

She called her permission to enter almost immediately , and his suspicions that she was still awake in spite of the late hour were confirmed when he found her sitting up in bed, laptop open and a game of solitaire in progress."Hey."

She smiled at him."Nice pyjamas.Are we having a sleepover?"

John glanced down at his clothing, taking in his sweats and t-shirt."I was sleeping," he started self-consciously."I—"

He wasn't sure what to say._I had a bad dream and needed to make sure you're okay_?Yeah – John didn't think so.

The smile faded slowly from Elizabeth's lips as he stood silently.After several moments she set her laptop on her bedside table and stood, coming to stand before him in the middle of her room."What's wrong?"

He shook his head in automatic denial."Nothing."

She gave him that look."John."

He offered her a crooked half-smile in response.Still unsettled from the nightmare, he reached out and gently touched her arm."How are you?"

Elizabeth tilted her head as she searched his face."I'm fine.Keller and Heightmeyer will back that up."Her fingers grazed his cheek."Why are you here, John?"

"I can go."He deliberately misunderstood her meaning.

She scowled at him."That's not what I meant and you know it."

He stared at her, at this woman who was standing here in front of him in spite of all the odds, and he gave in to the yearning he'd had the past several days – hell, past several _years_, if he was being honest with himself.Leaning forward, he touched his lips to hers.

The kiss was chaste, but there was no mistaking the intent behind it. After just a few moments John pulled back, but then Elizabeth leaned up and their second kiss was anything but innocent.His arms slid around her waist and she took a step closer so that her chest brushed his, sliding a hand around to the back of his head to hold him to her.She made a quiet sound when his tongue stroked over her lips and John tensed with arousal.He took an instinctive step forward, then another and another until he'd backed her across the room and they crashed into something solid, the force of it pressing their bodies flush against each other.His hips moved into hers and she whimpered, one hand fisting in his shirt, the other sliding just beneath the waist of his sweats.

He forced himself to pull away, resting his palm against Elizabeth's flushed cheek and brushing his thumb over her lips, wet and red and _he did that to her_."I should go."

"Stay."

He hesitated."I really should—"

"Stay, John."

He stayed.

**

In the middle of the night, John woke to the sound of Elizabeth screaming.

He was out of bed in a second, and had the lights on before another three had passed.It took several more before his eyes adjusted to the sudden brightness.

Elizabeth was curled into a ball on her side, hands clamped over her head and her eyes screwed shut.And she was still screaming, unearthly shrieks that didn't even sound human.

After calling her name several times and getting no response, John scrambled to find his headset."Medical emergency in Dr. Weir's quarters!" he barked, then yanked on his sweatpants before trying to get Elizabeth's attention once more.

He doubted it had anything to do with his efforts but she had stopped screaming by the time the medical team arrived.She was still curled in on herself and hadn't opened her eyes, but her cries had faded to whimpers that left him feeling helpless.

"What happened?" someone asked over the roar of blood in his ears, and John shook his head.

"I don't know.We were asleep and the next thing I know she's screaming, like...."He faltered; he had no idea what could prompt a sound like that."She hasn't said anything.I'm not sure she even knows we're here."

Another quiet whimper caught his attention and John slipped between the people working on Elizabeth.He took her hand, careful of the equipment that was already attached to her, and rubbed his thumb over her knuckles.Maybe she'd know he was there.

"Hurts."

The word was barely more than a breath, almost inaudible against the noise of the medical team."What hurts, Elizabeth?" he asked, bringing her hand to his chest.

"Head," she whispered."Too many voices.So many...."

She trailed off and John thought she might have fallen asleep; at least, he hoped it was only sleep.

The med team loaded Elizabeth onto a stretcher and John looked around fleetingly for his t-shirt before remembering that Elizabeth had claimed it to sleep in a few hours earlier.

Bare-chested and acknowledging that there would be no escaping the rumour mill anyway – and that at the moment, he couldn't care less – John followed the swiftly moving group towards the infirmary.

**

"Has there been any word?"

John blinked tiredly at Teyla."She's stable, whatever that means."He nodded a greeting to Ronon, who threw him a t-shirt before flopping into a nearby chair."They're running a bunch of tests."_For all the good that seemed to do_, John reflected bitterly before forcing the thought away.

"We will wait with you."

"You don't have to—"His protest died at the gentle touch of Teyla's hand on his forearm."Right.Okay."She started to pull away but he caught her fingers with his own before she withdrew completely, squeezing his thanks.Then he settled back in the chair, letting his head thunk against the wall behind him as his eyes slipped closed.

He didn't know how long he drifted before quiet footsteps and Keller's voice had him snapping awake."Colonel Sheppard?"

He stood, looking at her silently.

She cleared her throat."Dr. Weir is asking to see you."

John merely nodded as he pushed his way past the doctor, hearing Teyla ask after Elizabeth as he made his way to her bedside.God, he'd already spent too much time here.She didn't deserve this.

Her eyes were closed when he approached and he paused, suddenly unsure.But then she looked at him, brightening at the sight of him, and all his uncertainty disappeared.

"How're you doing?"He took her hand, using the other to brush her hair off her face before leaning down to kiss her forehead.

"They're coming, John."He pulled back a little to study her face; she was pale but alert, her expression somewhere between fearful and determined."The Asurans.They've found us, and they're coming."

"How do you know?"He wasn't sure he wanted to know the answer.

She lifted the hand he wasn't holding and touched the side of her head."I can hear them."

**

John strode into the briefing room and started talking before he'd even sat down."Here's where we are," he started, and the little bit of chatter in the room died immediately."For those of you who might not know, Dr. Weir was admitted to the infirmary at about 0400 with a severe migraine due in part to 'voices'.At 0500 she informed me that the voices she heard were those of the Asurans, who have pinpointed our location and are not only in pursuit, but gaining on us.Tests confirm the presence of nanites in Dr. Weir's brain.I don't pretend to know what's going on, but apparently it's plausible that she is, somehow, 'hearing' them."

To his left, McKay straightened."Well you see—"

"Not now."John cut him off with a curt wave, looking around.Gathered around him were his team and Lorne's, everyone watching him with similar expressions of solemnity."Best guess is we have a day, maybe two, before they reach us.We can't outrun them and with our depleted ZPM power we wouldn't withstand a tactical assault for more than a few hours."He paused for a second to let that sink in.Then he leaned forward."We need options."

**

Their meeting was interrupted three hours later by Chuck, who sounded wary."Colonel Sheppard, sir?"

John stepped away from where two Marines were arguing the merits of using cloaked puddle jumpers to deliver bombs to the Asuran ship.He touched his earpiece."Go ahead."Chuck had been instructed not to disturb him except for emergencies, so this couldn't be good.

"Dr. Keller is looking for you, sir.Dr. Weir is missing."

John's hands clenched."What do you mean, _missing_?"

"She left the infirmary and no one knows where she's gone.She's not answering her radio."

John swore under his breath; with those nanites in her head, Elizabeth was potentially a security risk.He should have posted a guard by her bed._Shit_.

"Lock down the city," he instructed, catching Teyla and Ronon's eyes and jerking his head toward the door."Order off-duty and non-essential personnel to their quarters and have everyone else check in.Compare the locations of confirmed personnel with lifesigns readings and let me know of any discrepancies.Sheppard out."He shifted his attention to Ronon and Teyla."Elizabeth's missing.There's no way of knowing if she's still... _her_."His teammates nodded and moved for the exit without a word.John breathed in."Be careful," he said softly, and he wasn't talking entirely about their own safety.

**

A half-hour of fruitless searching was interrupted by Chuck."Colonel Sheppard?We think she might be in a lab near the west pier."

John frowned, not sure what to make of that. It was something of a relief to finally have an idea where she might be, but he couldn't imagine why she would be in an abandoned lab.

With the transporter, it only took him five minutes to reach the lab almost halfway across the city.He paused at the door only long enough to draw his weapon and then entered without waiting for backup.

She was standing with her back to him, looking like she was working on something though he couldn't say what, since it was blocked by her body."Elizabeth?"

She glanced over her shoulder."John."Her inflection seemed a bit off but she turned back to whatever she was doing without saying anything else.Maybe he'd imagined it.

John readjusted his grip on his weapon and licked his lips."Elizabeth, I need you to step away from the bench."

She kept working."I can't.I have to finish."

John closed his eyes briefly."Finish what?"

She hesitated."I'm not sure.I just know that I have to complete it now."

"Eliz—"

"There's no time!"She spun to face him, her expression equal parts determination, desperation, and fear."Please, John.Let me finish."

"I can't."He cut off the protest he could see coming."You don't even know what you're building.You've got nanites in your head and you're hearing voices.I can't just let you keep working on something that could blow up the city for all you know."

She went rigid for a moment and then all of a sudden slumped."You're right," she murmured.She set the tool in her hand carefully on the bench and took several halting steps in his direction.John activated his radio as he moved to meet her halfway."Teyla, Ronon, I've got Elizabeth."He reached out to touch her arm, surprised to find her shaking.After a glance at the machine she'd been building he added, "Find McKay and get him to the lab in the west pier."Shifting his attention back to the woman in front of him he asked, "You okay?"

She made a face at him."Stop asking me that."

"Stop doing things that make me ask."They grinned at each other but the moment of levity quickly passed."Why are you here?"

Elizabeth shook her head, stepping away.They both looked at the mostly built machine sitting on the bench.She sighed."I don't know.I was sitting in the infirmary waiting to hear the test results when I got this... _urge_.A compulsion.I needed to come here.I needed to build that machine.I don't know what it is or what it does but I know exactly what I need to do to create it.It's right here.Step by step."She touched her temple.

John didn't know what to say or do in response to that.He started pacing around the lab, frustrated at all the things out of his control lately.

He heard McKay before he saw him, complaining that he had more important things to deal with than an abandoned Ancient lab."Over there," John said the instant Rodney came into sight, waving a hand in the direction of the bench."We need to know what that thing is and if it poses a threat."

Rodney gaped at him for a second."This lab was inventoried last year.What could possibly warrant bringing me down here when I could be instrumental in coming up with a plan to defeat the Asurans?"

"Would you just do it already?"John asked irritably, exchanging a look with Ronon, who had escorted McKay.

Ronon smirked as Rodney grumbled his way over to the bench.Off to the side, leaning against the wall with her arms folded over her stomach, Elizabeth watched without a word.

John waited impatiently as McKay poked around and muttered to himself.He found some instruments on the other side of the lab and took them back to Elizabeth's machine to take readings, or so John presumed.Then McKay jerked upright, dropped his instrument, and spun around; John prepared to hear that they had a bomb on the verge of exploding.That wasn't quite what McKay had to share, however.

"It's a ZPM," he said, sounding awed."It's not quite functional and it's not of typical Ancient design but the underlying principles appear to be the same.Where did it come from?"

John jerked his thumb at Elizabeth."She built it," he said wearily, somehow unsurprised that a woman who didn't understand Rodney's technobabble any better than he did had built a ZPM from scratch in just a few hours.

McKay rounded on Elizabeth, looking like he was about to have a stroke."You?You _built_ this?But—"He stared at her, the ZPM, then Elizabeth again."But _how_?"

She looked exhausted."I was hoping maybe you could tell me."

**

"We have a plan."

John raised an eyebrow when Rodney didn't continue."Well?" he prodded, impatient.They didn't exactly have time to waste.

Rodney seemed to be in a grandstanding mood."What are the Asurans flying?"

John frowned."Is this a trick question?"At Rodney's expression he sighed and said, "A ship?"

"But what _kind_ of ship?"

"…One that looks like Atlantis?"He took a shot in the dark, not knowing what Rodney was getting at.

Apparently, he got it right because McKay snapped his fingers and pointed at him, a clear sign of excitement."Exactly!"

John had had enough."Get to the point, McKay."

Rodney sulked for a bit but then quickly began explaining his idea."The Asurans built their ship in Atlantis' image, but it's not an Ancient design.We think it's likely that their ship was built using nanotechnology – essentially, it's composed of inert Replicator 'blocks'."

"How does this help us?"

"The composition of the blocks should match the composition of the nanites that make up the Asurans themselves, which means that the city should be vulnerable to the same weapon that deconstructs the Asurans to their base elements.If we can focus a large enough beam on their ship, it should disintegrate into trillions of tiny, useless pieces."

John looked to Zelenka."You agree with this?"He'd learned early on that Rodney tended to have way too much faith in his "brilliant" ideas, whereas Radek was often overly pessimistic.The truth usually lay somewhere between the two men's opinions.

Zelenka's response surprised him."It should work.The problem lies in constructing a directional beam large enough and powerful enough to deconstruct the entire ship."

"But," Rodney continued, "between my knowledge of Atlantis' systems and Elizabeth's freaky new ability to navigate the computer mainframe, we should be able to modify the beam that we used when we saved General O'Neill and Woolsey."

When they came right down to it, John thought, they didn't really have a choice."Do it."

**

He was reading through the latest reports of Atlantis' repairs when a knock at the door drew his attention.He looked up to find Elizabeth hovering at the entrance to her own office and waved her in."Hey.Why'd you knock?"

She shrugged, sitting in one of the chairs she had for visitors."You looked busy. I didn't want to bother you."

He heaved a melodramatic sigh as he spun the laptop around so she could see the screen."Just wading through reports.How long 'til Keller returns you to duty so I don't have to do this anymore?"

The smile he'd managed to get from her at his complaint disappeared, leaving her looking drawn and pale.In her lap, her fingers were twisting together, a sure sign of her anxiety."That's sort of why I'm here."

John turned the laptop back around and lowered the lid, pushing it aside."What is it?"

She was still coiling her fingers into knots."I've been thinking about the Asurans and how they were able to find us."She drew a breath, avoiding his gaze."I think it's my fault."

John shook his head, not following her reasoning."How is it your fault?"

She closed her eyes and lowered her head."I think they can sense me the same way I can sense them.I can't prove it, but I know it's true.I can _feel_ it."One hand touched her chest lightly, above her heart.

John stood so abruptly that his chair rolled back and crashed into the wall behind him.The sudden need to move was overwhelming and he began to pace the length of the office, running through the ramifications of this new information in his head.This could be very, very bad.

"Can they read your thoughts?" he asked eventually, trying to determine just how much trouble Atlantis was in.

"I don't know.I don't think so, but I can't be sure."

Her voice was quiet, almost faint.John paused to look at her and realized she had folded in on herself, practically huddled in the chair.Questions and fervent pacing weren't what she needed from him right now, he berated himself.Slowing, he dropped into the chair next to Elizabeth and reached across the space separating them to touch her knee."I'm sorry."

She shook her head quickly."'S'okay."

"No, I mean—"God, this whole situation was so fucked up and it was all because of him."I'm sorry for this.All of this.It's my fault."

"John, it's not—"

"It is!All of it.If I'd listened to you instead of Ellis, if I'd gotten the city's shields up just a few seconds sooner, if I'd headed for Earth instead of picking a random direction...."He studied her face, reaching to brush a lock of hair from her cheek."I'm the one who authorized using the nanites."She knew that, of course, but they'd never discussed it.

Elizabeth took his hand and John squeezed it so hard, he had to be hurting her."It's not your fault."She sounded so certain and he wanted so desperately to believe her."When you agreed to Ellis' plan you were doing what you thought was right, what you felt would protect us and Earth.You did what you could to keep Atlantis safe and to get the away from danger."She ran her thumb over the back of his hand."And I can hardly blame you for choosing to try the nanites.I wouldn't be here right now if it weren't for you."

In his mind he could still see her lying so still and pale in the infirmary, could hear Keller telling him Elizabeth's injuries were too severe and that there was no chance of her ever waking, and he wondered for the millionth time if he'd been too selfish in the decision he'd made.She was here and whole and _her_, but she was also doing things without knowing how or why and hearing voices and in pain.He'd never stop blaming himself for that, he knew.

"Hey."Elizabeth squeezed his hand and he looked up at her, deciding he had no right to feel sorry for himself when sitting next to her."You've done everything you could to keep everyone safe, not just the past few weeks but the past three years.Atlantis never would have made it this far without you, John.Never think for a second that I've ever regretted asking you to come."

John wished severely that they were anywhere except the glass-walled office because at that moment, all he wanted to do was kiss her senseless and there was no way she'd let him do that with a potential audience just across the walkway.He settled for a grossly inadequate and embarrassingly tremulous "Thank you," wondering how he'd managed to find complete trust from this woman three galaxies away from the life he'd known.

After an awkward silence John cleared his throat and changed the subject."So, McKay and Zelenka think they've got a plan figured out," he began.Their hands separated and he sat back, trying to clear his head."They think we can modify the jumpers to emit a directional beam; by surrounding the Asuran vessel and having all the jumpers fire simultaneously, we should be able to destroy their ship."

"How long until the jumpers are ready?"She followed his lead, letting their conversation turn back to work.He wondered if she knew what that meant to him.

"They've already started the modifications.Rodney says they should be ready early tomorrow."

She nodded."I'm going up with you."

"Elizabeth—"

"I'm going, John.I have to be there."

Damn stubborn woman."Fine.But you're staying back with Rodney."

She tilted her head in acknowledgement, then yawned so widely he thought he heard her jaw pop."How long has it been since you last slept?"

One eyebrow arched."Not as long as it's been for you."

She had a point, he conceded.When he did the math, he figured he'd been up for nearly thirty hours.Before that, he'd only gotten a few hours of sleep before his very long day had begun with the sound of Elizabeth's screams."Now that you mention it –" he stood, offering Elizabeth his hand to pull her to her feet "—it has been a pretty long day."

"Off to bed, then?" she asked with an impish smile, the one with the dimples.

Prospective audience or not, he risked resting his hand against the small of her back as they left the office.She let him."Well, that's one idea.But you know, I'm not really all that tired."

"Is that right."John could have sworn there was a little extra swing to her hips as they headed for the living quarters."Well, I'm sure we can find a way to fix that."

**

At 0700 the next morning, John set his puddle jumper in position and triple checked his controls.Satisfied that everything was ready and there was nothing more he could do until the Asurans arrived, he hit the radio switch."McKay?How's it look?"

There was no answer for several seconds and the usual nervous anticipation he experienced before missions ratcheted up a few notches."McKay?"

The answer, when it came, was not exactly reassuring."Something's not right."

"Care to be a little more specific?"

"I don't know.Something's off about the sensor readings."

"Are they still coming?"

"They're definitely headed here. But there's something...."He trailed off for a second and then added, "Be careful, Colonel."

"Always am," he said flippantly.The conversation ended with the familiar blue flash of a ship exiting hyperspace.

Except it wasn't a ship, at least, not the single city-ship they'd all been expecting.Instead, a smaller vessel shot into view, followed by another and another and another until John lost count."McKay! What the hell is going on?!"

Rodney sounded panicked."I don't know!The Asurans must have re-structured their city into dozens of smaller ships."

More quietly, he could hear Elizabeth."There are hundreds of them."

McKay had apparently forgotten he was on the radio."They'll be killed."

"Thanks for the vote of confidence, McKay!"Then someone fired the first shot and there was no more time for conversation.

As he always did during battle, John became singularly focused on his target.His sight narrowed to the information his HUD showed him, his mind clear and empty but for the lightning-quick equations needed to lock on to the enemy and fire.Nothing existed except for him and his prey.

It could have been minutes or hours later – time held no relevance when he was in this state of mind – that the world outside the space battle was abruptly brought back into sharp focus by Ronon's voice."There are intruders in the 'gate room."

"In the infirmary as well."Teyla.

"I'm getting reports of Asurans in the mess hall, living quarters, and the east pier."Chuck.

_Shit_.John took a quick recon of their situation, weighing the threat of the Asuran ships against the threat of the Replicators in Atlantis.With the number of civilians in the city, there wasn't much of a choice.Hopefully Elizabeth's ZPM would hold off the fleet long enough for them to deal with the invaders.

An Asuran ship appeared out of nowhere and John rolled his jumper one hundred and eighty degrees to starboard, firing off a shot that hit the other vessel dead center, blasting it into a shower of harmless silver bits.He hit the radio. "This is Jumper One.All pilots, fall back to Atlantis.Repeat, fall back to Atlantis."

Acknowledgements trickled in but John ignored them, concentrating on ducking and weaving his way through ships and weapons' fire.He managed to destroy two more Asuran vessels before reaching the jumper bay, but there were still too many of them.

The rear hatch of the puddle jumper hadn't even completely lowered before John exited, ARG in hand.He shared a quick look with Elizabeth and Rodney, who'd landed ahead of him."Control room."They both nodded.

Halfway there they met up with Teyla and Ronon; she looked calm, he looked angry."Dr. Zelenka requests Dr. McKay's assistance in the lab.He believes he can adjust the beam to fire in a burst rather than directionally."Teyla didn't look like she really understood Zelenka's explanation, but that didn't matter.

McKay looked equally excited and terrified."You can't expect me to go to the lab by myself when there are intruders!Do you have any idea how screwed you would all be if one of those things stuck its hand in my head and read my mind?I know more about this city than anyone!"

Except Elizabeth, John thought, but he didn't have time to worry about that just then."Teyla will get you there.Call me as soon as you know something."He shifted his attention to Ronon, already tuning out McKay's protests."You're with us."Ronon merely nodded.

The three of them made their way down to the control room, managing to kill a few Asurans along the way.The sounds of ARGs and whatever weapons the Asurans used was almost constant now and not too far off, John heard someone scream.

There was a sudden boom, echoed by the shaking of the city, violent enough to throw John into the wall.Chuck's voice filtered through the rumbling before John could demand a report."There's been an explosion in the engine room!Shields are down to less than a third of full strength!"

"McKay!" John shouted over the headset."When the hell will that weapon be ready?!"

"We can't do it!That kind of focused power burst would overload the ZPM and destroy Atlantis!"

They were officially out of options.They were outnumbered and overpowered and though not a single member of the Atlantis expedition would surrender without a fight, it was only a matter of time.John couldn't see a way out of this.

The whine and roar of weapons surrounded them, closer and louder than ever, but he could still hear Elizabeth as clearly as if they were chatting over coffee in the mess hall in the middle of a sleepless night."I have to leave Atlantis."

He froze."You can't."

"The Asurans are here because of me.They found Atlantis because of _me_.If I stay, you'll never be safe from them."

"You _can't_."His voice cracked.

"I don't have a choice."She sounded confident, decisive, but he could see the tears in her eyes."When I leave, you'll have a chance.Right now I'm a bigger threat to them than you are.They'll come after me and leave Atlantis alone."She dropped to a near-whisper but he could still hear every word she said.He almost wished he couldn't."You have to let me go, John."She held his gaze until nearby weapons' fire caused a shower of sparks overhead.He ducked instinctively, covering his face for a second.By the time he straightened again Elizabeth was halfway up the stairs.

"Elizabeth!"Beside him, Ronon tensed, then twisted and took out an Asuran with a single shot.John hardly noticed."_Elizabeth_!"

She didn't so much as pause.

Too late, John chased her up the stairs; by the time he reached the control room she had used her newfound knowledge of the city's systems to raise a shield none of them had known even existed, blocking the control room and the 'gate from his reach.Already she was moving down the main staircase, toward the active Stargate.

John swore, racing back down the stairs he'd just come up to approach the 'gate room from the side, where the shield brought him up short."Elizabeth!"

She slowed, then stopped just a few steps from the 'gate's water-like surface.He saw her take a breath before she twisted to face him across the empty space.

He couldn't hear her – or maybe she never spoke aloud – but he understood her anyway.

"Me too," he whispered back, catching her sad smile before she turned and walked through the shimmering horizon.The 'gate and the shield protecting it both shut down.Not long after that, the sounds of fighting died down as the Asurans beamed out of the city, abandoning Atlantis and her inhabitants for more dangerous prey.

Alone in the middle of it all, John stood stock still, eyes still fixed on the empty space in front of the Stargate.Then he sighed and turned to start picking up the pieces of his city.

"Me too."

_\--end--_

__


End file.
